A versatile environment for 3D complex tissue modeling and light simulations based on Blender

Abstract

Rapid advances in emerging medical imaging techniques require advanced model-based computational approaches to obtain functional and structural information from increasingly complex and multi-scaled anatomies. The lack of efficient tools to accurately model the anatomical structures of tissues, and subsequently perform quantitative multi-physics modeling greatly impede the clinical translation of these emerging modalities. In the field of biophotonics, while the Monte Carlo (MC) method has been widely adopted for simulating light transport in biological tissues, the utility of such method is largely limited to simple domains. Recent development in mesh-based Monte Carlo (MMC) method expands our capabilities in simulating complex tissues by using tetrahedral meshes, however, the mesh generation of such structures often requires specialized meshing tools, such as Brain2Mesh and Iso2Mesh. A simplified and intuitive interface for tissue anatomical modeling and optical simulations is essential to make these advanced modeling tools broadly accessible to the user community. This thesis responds to the above challenge by combining powerful open-source 3-D modeling software Blender (\url{http://blender.org}) with state-of-the-art 3-D mesh generation and MC simulation tools, utilizing the intuitive and interactive graphical user interface (GUI) in Blender as the front-end to allow users to create complex tissue mesh models, and subsequently launch accurate MMC light simulations. Towards this goal, we have developed a Python-based Blender plugin -- BlenderPhotonics -- to interface with Iso2Mesh and MMC. The developed interface allows users to create, configure and refine complex simulation domains and run hardware-accelerated 3-D light simulations. This framework can be easily extended for other multi-physics modeling tasks such as finite-element analyses (FEA) of tissue mechanical deformation, electromagnetic (EM) forward and inverse scattering, and heat-transfer modeling.--Author's abstract